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16012 Commits

Author SHA1 Message Date
Axel Kohlmeyer d1255ab572 we are LAMMPS, not LIGGGHTS 2018-11-22 09:22:09 -05:00
Axel Kohlmeyer 5efd8c06b1 correct formatting for examples when discussing the non-incremental nature of special_bonds 2018-11-22 06:25:39 -05:00
Axel Kohlmeyer 900ecc170a document that rcb balancing depends on comm_style tiled which in turn is not compatible with triclinic cells 2018-11-21 16:08:24 -05:00
Axel Kohlmeyer 689334706f Merge branch 'more-small-changes' of github.com:akohlmey/lammps into more-small-changes 2018-11-21 09:24:21 -05:00
Axel Kohlmeyer a91d89b516 avoid array overflows and silence compiler warnings from unused parameters 2018-11-21 09:24:10 -05:00
Axel Kohlmeyer 385cf2e1fc avoid array overflows and silence compiler warnings 2018-11-20 22:40:46 -05:00
Axel Kohlmeyer 090fc7bc8a remove unused sphinx-images extension from virtualenv setup 2018-11-20 22:14:24 -05:00
Axel Kohlmeyer d359beb170
Merge pull request #1215 from jrgissing/bond/react-doc-corrections,mostly-formatting 
Bond/react doc corrections,mostly formatting
 2018-11-20 10:50:55 -05:00
Axel Kohlmeyer 719f719496
Merge pull request #1216 from bondrewd/charmm2lammps 
make topology parsing in charmm2lammps.pl more tolerant
 2018-11-20 10:35:52 -05:00
Axel Kohlmeyer 421f97e444
Merge pull request #1214 from akohlmey/collected-small-changes 
Collected small changes and many spelling fixes for next release candidate
 2018-11-20 10:34:58 -05:00
Axel Kohlmeyer 9f960baa4f restore USER-ATM package data files taken from CVS repo 2018-11-20 09:17:02 -05:00
Axel Kohlmeyer 981f56840e update workflow tips for checking new LAMMPS contributions 2018-11-20 00:30:45 -05:00
Axel Kohlmeyer 4c021dad37 port spell fixes to source code 2018-11-20 00:09:11 -05:00
Axel Kohlmeyer 4251c70e93 update list of false positives for spellchecking 2018-11-20 00:08:07 -05:00
Axel Kohlmeyer 0bcb1bd301 more spelling fixes and occational re-edits 2018-11-20 00:06:40 -05:00
Axel Kohlmeyer c6c00ee7ee more spelling fixes 2018-11-19 20:46:32 -05:00
Axel Kohlmeyer 6f7b052e24
update comments and remove commented code 2018-11-19 16:38:25 -05:00
Diego Ugarte 9b401b6ed0 fix topology parsing 2018-11-20 06:22:32 +09:00
Axel Kohlmeyer b34dac41c2 port documentation spelling fixes to comments or strings in source code. 2018-11-19 16:15:24 -05:00
Axel Kohlmeyer 13ae678f39 more manual spelling fixes 2018-11-19 16:13:57 -05:00
Axel Kohlmeyer 8a94a32551 avoid duplicate label 2018-11-19 15:19:23 -05:00
Axel Kohlmeyer b6f0fe4c2d more changes for correct and consistent spelling in the manual 2018-11-19 11:47:33 -05:00
Axel Kohlmeyer 809bd855b6 adjust wording of non-features discussion to be more in-sync with recent developments 2018-11-19 11:24:55 -05:00
Axel Kohlmeyer 4dc2f9c6c4 fix some spelling errors in the manual 2018-11-19 11:24:17 -05:00
Axel Kohlmeyer c49c35e41d avoid tuncation error through integer division and promote to use "bigint" instead of "int" to avoid overflows for large systems 2018-11-17 06:40:33 -05:00
Axel Kohlmeyer 1597e78d5a guarantee initialization of hyperflag 2018-11-17 06:39:28 -05:00
Axel Kohlmeyer a7bfb30043 update atc/cauchy_born examples with missing files 2018-11-16 23:03:47 -05:00
jrgissing 1d4e1f1425 bond/react:doc corrections 2018-11-16 20:47:51 -07:00
jrgissing d7abb8cf4d Revert "bond/react: doc corrections, mostly formatting" 
This reverts commit da88305f4d.
 2018-11-16 20:42:52 -07:00
jrgissing da88305f4d bond/react: doc corrections, mostly formatting 2018-11-16 20:41:49 -07:00
Jacob Gissinger 177a5ddb7a
Merge pull request #34 from lammps/master 
rebase
 2018-11-16 20:29:46 -07:00
Axel Kohlmeyer bbcb659158 render fix commands in 6 columns instead of 8 so only narrow screens need to scroll horizontally 2018-11-16 22:09:07 -05:00
Axel Kohlmeyer dc6054fc2d rename "All commands" headers to "General commands" 2018-11-16 22:04:35 -05:00
Axel Kohlmeyer 0264edfcec provide example for how to set Tdamp correctly to 100 timesteps for all choices of unit 2018-11-16 16:27:47 -05:00
Axel Kohlmeyer a66384cfea update github tutorial/howto for recent changes in the development workflow 2018-11-16 16:27:05 -05:00
Axel Kohlmeyer fd4262805d for enabling MPIIO we also need to set -DLMP_MPIIO 2018-11-16 15:48:35 -05:00
Axel Kohlmeyer 0d72c3769d
Merge pull request #1212 from stanmoore1/git_doc 
Tweak to github-development-workflow.md
 2018-11-16 12:44:58 -05:00
Axel Kohlmeyer 177733ecdd
Merge pull request #1211 from lammps/doc-hyper 
change warning to just a note
 2018-11-16 12:11:54 -05:00
Axel Kohlmeyer 0b60bf65d1
Merge pull request #1210 from giacomofiorin/colvars-update 
Update Colvars library to version 2018-11-16
 2018-11-16 12:00:41 -05:00
Steve Plimpton c5c26abdd3 change warning to just a note 2018-11-16 09:26:37 -07:00
Stan Moore 5974741eea Tweak to github-development-workflow.md 2018-11-16 09:26:12 -07:00
Axel Kohlmeyer d8f540a433
Merge branch 'master' into colvars-update 2018-11-16 11:24:10 -05:00
Axel Kohlmeyer 0a96b891ef
Merge pull request #1209 from pdebuyl/fix_cmake_h5md 
fix cmake build for USER-H5MD
 2018-11-16 11:22:45 -05:00
Giacomo Fiorin 11de8dafe3 Update Colvars library to version 2018-11-16 
Fixes several issues with running averages and time correlation function
computations.  Details are in:

https://github.com/Colvars/colvars/issues/143
https://github.com/Colvars/colvars/issues/193
https://github.com/Colvars/colvars/pull/194
 2018-11-16 09:57:07 -05:00
Pierre de Buyl 2c979e878f fix cmake build for USER-H5MD 
The hdf5 includes were needed as well for building the dump.
 2018-11-16 15:18:58 +01:00
Axel Kohlmeyer cf79751f4f
Merge pull request #1207 from akohlmey/next-patch-release 
Patch release 15 November 2018
 2018-11-15 19:33:52 -05:00
Axel Kohlmeyer e4dee3de17
Merge pull request #1206 from akohlmey/collected-small-changes 
Collected small changes for next release
 2018-11-15 17:29:26 -05:00
Axel Kohlmeyer 6e225d90fc fix some minor bugs write data file writing and remove dead code and silence compiler warnings 2018-11-15 16:50:56 -05:00
Axel Kohlmeyer 1fc3b4618c remove dead code and silence compiler warnings 2018-11-15 16:50:56 -05:00
Axel Kohlmeyer eae9d27f6d OpenMP support from the compiler is not a requirement for USER-OMP. Without OpenMP, it is like the OPT package but for many more styles, so it is still useful and should be supported. 2018-11-15 16:50:56 -05:00